species:   Cocin
pid:       PID1283
parent:    cci-milR-28
paralog:   
locus:     scaffold_392:9771-9828
matures:   ['UAGGAUUCGACGAUGGCG', 'CCAAUGUUGAACCCUAGAUCGC']
srr:       SRR9972092
genome:    /Users/jax/+Genomes/Fungal_genomes/Cocin.Copci_AmutBmut1_AssemblyScaffolds.fa
alignment: /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lau2020-gn.SRR9972092.cram
call:      samtools view /media/data/njohnson/+SeqLibraries/FunHP_libraries/Lau2020-gn.SRR9972092.cram scaffold_392:9771-9828

2 out of bounds
16 alignments
11 proper strand
10 stranded perfect matches

******************               ************************ 
UAGGAUUCGACGAUGGCGAGAGGGACCUGCCUCGUCCAAUGUUGAACCCUAGAUCGCU
((((.(((((((.(((...((((......))))..))).))))))).)))).......
UAGGAUUCGACGAUGGCG---------------------------------------- l=18 a=4 c
-----------------------------------CCAAUGUUGAACCCUAGAUCGC- l=22 a=0 c*
UAGGAUUCGACGAUGGCG---------------------------------------- l=18 a=4 ma
-----------------------------------CCAAUGUUGAACCCUAGAUCGC- l=22 a=0 ma*

UAGGAUUCGACGAUGGCG---------------------------------------- l=18 a=4 (c,ma)
UAGGAUUCGACGAUGGCa---------------------------------------- l=18 a=1 
UAGGAUUCGACGAUGGCGA--------------------------------------- l=19 a=2 
UAGGAUUCGACGAUGGCGAG-------------------------------------- l=20 a=2 
UAGGAUUCGACGAUGGCGAGA------------------------------------- l=21 a=1 
UAGGAUUCGACGAUGGCGAGAG------------------------------------ l=22 a=1 

mb-00011
ax-1001001
ku-01
ss-101010101000
fn-101
